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OrthoFinder is a fast, accurate and comprehensive analysis tool for comparative genomics. It finds orthologues and orthogroups infers rooted gene trees for all orthogroups and infers a rooted species tree for the species being analysed. OrthoFinder also provides comprehensive statistics for comparative genomic analyses. OrthoFinder is simple to use and all you need to run it is a set of protein sequence files (one per species) in FASTA format.


GNU GPL v3, https://www.gnu.org/copyleft/gpl.html


Upcoming modulesystem change alert!

Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.

You can test the new version now by adding a line

source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules

to your script before loading a module. Then, you can list all versions of orthofinder and load default version of orthofinder as

module avail orthofinder/ # list available modules
module load orthofinder   # load (default) module

If you wish to keep up to the current system, it is still possible. Simply list all modules by

module avail orthofinder

and choose explicit version you want to use.


Official website: https://github.com/davidemms/OrthoFinder

Official documentation: https://github.com/davidemms/OrthoFinder#running-orthofinder

Original paper: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0721-2